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Tn5041-like transposons: molecular diversity, evolutionary relationships and distribution of distinct variants in environmental bacteria^bc

Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia¹
School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK²

Author for correspondence: G. Kholodii. Tel: +7 095 196 0015. Fax: +7 095 196 0015. e-mail: kholodii{at}img.ras.ru

A detailed study on the geographic distribution, molecular diversity and evolutionary relationships of 24 closely related variants of the Tn5041 transposon found among 182 mercury resistant environmental Gram-negative strains from the IMG-Hg Reference Collection is reported here. RFLP analysis, followed by the determination of partial DNA sequences, identified 14 distinct types of these transposons, which differed from each other by 1–7 single-event DNA polymorphisms. No polymorphisms were detected at the right arm of the transposons except an insertion of a new mobile DNA element carrying a mer operon (named the mer2 cassette) within the Tn5041 mer operon. According to the model presented here, the insertion occurred via homologous recombination with a circular form of the mer2 cassette. A total of 8 point mutations, 1 internal deletion, 2 end-involving deletions, 3 mosaic regions and 2 insertions were detected at the left arm of the transposons. The insertions were a transposon closely related to Tn21 but lacking the integron and a new group II intron (named INT5041C). Inspection of the geographic distribution of the Tn5041 variants suggested that at least three long-distance waves of dissemination of these variants had occurred, accompanied by homologous recombination between different Tn5041 lineages. Movements of circular DNAs by homologous recombination as a source of mosaic genes and new mer genes, and formation of unusual mosaics ending or beginning at the Tn5041 att site are discussed.

View larger version (41K): [in this window] [in a new window]   Fig. 1. Tn5041 variants. The genetic/restriction map of Tn5041A together with the Southern hybridization probes 1 to 5 (described in Methods) are at the top. E, EcoRI; P, PstI; EV, EcoRV; Sc, SacII; orfP, the ORF encoding a porin-like protein; R’, an incomplete merR gene; , the minitransposon with terminal inverted repeats closely related to those of Tn5044 and Tn5046 (Kholodii et al., 2000a ; Mindlin et al., 2001 ; ACs Y17691 and Y18360); 1 and 2, the urf-1 (merE) and urf-2 genes. Other Tn5041 determinants are described in Introduction and Results. The thin lines represent unsequenced DNA; sequenced regions are shown by black bars (Tn5041 core sequence type), white boxes (regions of high divergence) and intermittent thick lines (documented by Yurieva et al., 1997 ; ACs Y09209 and Y09210). Shown on the right are the host strains and (in parentheses) the types of transposons. The point mutations are as follows: in position 811, GA eliminating the Tn5041 SacII site; 952, GA; 1240, deletion of G; 1241, CT; 1265, TC; 1384, CT; 2875, AG eliminating the Tn5041 EcoRV site; 3773, GA eliminating the Tn5041 PstI site. EV-, P- and Sc- are the EcoRV, PstI and SacII mutant sites. The insertions (symbolized by triangles) are located between nt 5439 and 5440 (all introns, INT), 6984 and 6985 (all mer2 cassettes), and 5900 and 5901 (Tn21In2 transposons). The LS47-4 deletion (100 bp) shown by // lies between nt 2394 and 3772. The orientation of INT5041 and the homologous segment of INT5041C are shown by arrows. The different sequenced regions are marked by lower-case letters. The examples, each representing identical allelic sequences, are deposited in the database. The set of the assigned ACs is as follows: a, AJ422111–AJ422116 and Y19000; b, AJ422117; c, AJ422126 and AJ422127; d, AJ422128 and AJ422129; e, AJ422223; f, AJ422227; g, AJ422228; h, AJ422229; i, AJ422230; j, AJ422233; k, AJ422231; l, AJ422232; m, AJ426649; n, AJ422130; the 1-containing region, Y19001. The sequences of the insertions and the adjacent regions are deposited with the database as single entries (the ACs are listed in Fig. 2 legend).

Abbreviations: AC, accession number; PMA, phenylmercuric acetate

^b The accession numbers for the nucleotide sequences reported in this work are given in the legends for Figs 1 and 2.

^c A comparison of the sequence of INT5041C with other proteins is available as supplementary data on Microbiology Online (http://mic.sgmjournals.org).

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